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Renamed softUnclipped functions to refCoord* 

These functions return reference coordinates, so they should be named accordingly.
This commit is contained in:
Mauricio Carneiro 2011-08-16 18:56:28 -04:00
parent ed8f769dce
commit 5d6a6fab98
1 changed files with 4 additions and 4 deletions
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8
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -631,8 +631,8 @@ public class ReadUtils {
*/ */
public static ReadAndIntervalOverlap getReadAndIntervalOverlapType(SAMRecord read, GenomeLoc interval) { public static ReadAndIntervalOverlap getReadAndIntervalOverlapType(SAMRecord read, GenomeLoc interval) {
int start = getSoftUnclippedStart(read); int start = getRefCoordSoftUnclippedStart(read);
int stop = getSoftUnclippedStop(read); int stop = getRefCoordSoftUnclippedStop(read);
if ( !read.getReferenceName().equals(interval.getContig()) ) if ( !read.getReferenceName().equals(interval.getContig()) )
return ReadAndIntervalOverlap.NO_OVERLAP_CONTIG; return ReadAndIntervalOverlap.NO_OVERLAP_CONTIG;
@ -658,7 +658,7 @@ public class ReadUtils {
return ReadAndIntervalOverlap.OVERLAP_RIGHT; return ReadAndIntervalOverlap.OVERLAP_RIGHT;
} }
public static int getSoftUnclippedStart(SAMRecord read) { public static int getRefCoordSoftUnclippedStart(SAMRecord read) {
int start = read.getUnclippedStart(); int start = read.getUnclippedStart();
for (CigarElement cigarElement : read.getCigar().getCigarElements()) { for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
if (cigarElement.getOperator() == CigarOperator.HARD_CLIP) if (cigarElement.getOperator() == CigarOperator.HARD_CLIP)
@ -669,7 +669,7 @@ public class ReadUtils {
return start; return start;
} }
public static int getSoftUnclippedStop(SAMRecord read) { public static int getRefCoordSoftUnclippedStop(SAMRecord read) {
int stop = read.getAlignmentEnd(); int stop = read.getAlignmentEnd();
List<CigarElement> cigarElementList = read.getCigar().getCigarElements(); List<CigarElement> cigarElementList = read.getCigar().getCigarElements();
CigarElement lastCigarElement = cigarElementList.get(cigarElementList.size()-1); CigarElement lastCigarElement = cigarElementList.get(cigarElementList.size()-1);